# All Classes and Interfaces

Class
Description
AbstractAlignmentMerger
Abstract class that coordinates the general task of taking in a set of alignment information, possibly in SAM format, possibly in other formats, and merging that with the set of all reads for which alignment was attempted, stored in an unmapped SAM file.
AbstractAlignmentMerger.UnmappingReadStrategy
AbstractIlluminaPositionFileReader
The position files of Illumina are nearly the same form: Pos files consist of text based tabbed x-y coordinate float pairs, locs files are binary x-y float pairs, clocs are compressed binary x-y float pairs.
AbstractInputParser
Class for parsing text files where each line consists of fields separated by whitespace.
AbstractMarkDuplicatesCommandLineProgram
Abstract class that holds parameters and methods common to classes that perform duplicate detection and/or marking within SAM/BAM/CRAM files.
AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
Little class used to package up a header and an iterable/iterator.
AbstractOpticalDuplicateFinderCommandLineProgram
Abstract class that holds parameters and methods common to classes that optical duplicate detection.
AbstractWgsMetricsCollector<T extends htsjdk.samtools.util.AbstractRecordAndOffset>
Class for collecting data on reference coverage, base qualities and excluded bases from one AbstractLocusInfo object for CollectWgsMetrics.
AccumulateQualityYieldMetrics
Combines multiple Picard QualityYieldMetrics files into a single file.
AccumulateVariantCallingMetrics
Combines multiple Variant Calling Metrics files into a single file.
AdapterMarker
Store one or more AdapterPairs to use to mark adapter sequence of SAMRecords.
AdapterPair
AdapterUtility
A utility class for matching reads to adapters.
AddCommentsToBam
A tool to add comments to a BAM file header.
AddOATag
AddOrReplaceReadGroups
Assigns all the reads in a file to a single new read-group.
AlignmentSummaryMetrics
High level metrics about the alignment of reads within a SAM file, produced by the CollectAlignmentSummaryMetrics program and usually stored in a file with the extension ".alignment_summary_metrics".
AlignmentSummaryMetrics.Category
AlignmentSummaryMetricsCollector
AlleleBalanceFilter
Filters out a record if the allele balance for heterozygotes is out of a defined range across all samples.
AlleleSubsettingUtils
Utilities class containing methods for restricting `VariantContext` and `GenotypesContext` objects to a reduced set of alleles, as well as for choosing the best set of alleles to keep and for cleaning up annotations and genotypes after subsetting.
AnnotationException
Exception thrown when loading gene annotations.
ArraysControlInfo
A simple class to store names and counts for the the Control Information fields that are stored in an Illumina GTC file.
AsyncIterator<T>
Wrapper around a CloseableIterator that reads in a separate thread, for cases in which that might be efficient.
AtomicIterator<T>
Describes
BafRegressMetrics
BaitDesigner
Designs baits for hybrid selection!
BaitDesigner.DesignStrategy
Set of possible design strategies for bait design.
BamIndexStats
Command line program to print statistics from BAM index (.bai) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinate.
BamToBfqWriter
Deprecated.
BarcodeEditDistanceQuery
A class for finding the distance between multiple (matched) barcodes and multiple barcode reads.
BarcodeExtractor
BarcodeExtractor is used to match barcodes and collect barcode match metrics.
BarcodeExtractor.BarcodeMatch
Utility class to hang onto data about the best match for a given barcode
BarcodeFileFaker
Created by jcarey on 3/13/14.
BarcodeFileReader
Reads a single barcode file line by line and returns the barcode if there was a match or NULL otherwise.
BarcodeMetric
Metrics produced by the ExtractIlluminaBarcodes program that is used to parse data in the basecalls directory and determine to which barcode each read should be assigned.
BaseBclReader
BaseCalculator
An interface that can take a collection of bases (provided as `SamLocusIterator.RecordAndOffset` and `SamLocusAndReferenceIterator.SAMLocusAndReference`) and generates a `ErrorMetric` from them.
BaseCallingProgramGroup
Tools that process sequencing machine data, e.g.
BasecallsConverter<CLUSTER_OUTPUT_RECORD>
BasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).
BasecallsConverter.ClusterDataConverter<OUTPUT_RECORD>
Interface that defines a converter that takes ClusterData and returns OUTPUT_RECORD type objects.
BasecallsConverter.ConvertedClusterDataWriter<OUTPUT_RECORD>
Interface that defines a writer that will write out OUTPUT_RECORD type objects.
BasecallsConverterBuilder<CLUSTER_OUTPUT_RECORD>
BasecallsConverterBuilder creates and configures BasecallsConverter objects.
BaseDistributionByCycleMetrics
BaseErrorAggregation<CALCULATOR extends BaseCalculator>
An interface and implementations for classes that apply a `RecordAndOffsetStratifier` to put bases into various "bins" and then compute an `ErrorMetric` on these bases using a `BaseErrorCalculator`.
BaseErrorCalculator
BaseErrorMetric
An error metric for the errors in bases.
BaseIlluminaDataProvider
Parse various formats and versions of Illumina Basecall files, and use them the to populate ClusterData objects.
BasicInputParser
TextFileParser which reads a single text file.
BciFileFaker
Created by jcarey on 3/14/14.
BclData
A class that implements the IlluminaData interfaces provided by this parser One BclData object is returned to IlluminaDataProvider per cluster and each first level array in bases and qualities represents a single read in that cluster
BclFileFaker
BclIndexFaker
BclIndexReader
Annoyingly, there are two different files with extension .bci in NextSeq output.
BclQualityEvaluationStrategy
Describes a mechanism for revising and evaluating qualities read from a BCL file.
BclReader
BCL Files are base call and quality score binary files containing a (base,quality) pair for successive clusters.
BedToIntervalList
BestEndMapqPrimaryAlignmentStrategy
For an aligner that aligns each end independently, select the alignment for each end with the best MAPQ, and make that the primary.
BestMapqPrimaryAlignmentSelectionStrategy
This strategy was designed for TopHat output, but could be of general utility.
BpmToNormalizationManifestCsv
A simple program to convert an Illumina bpm (bead pool manifest file) into a normalization manifest (bpm.csv) file The normalization manifest (bpm.csv) is a simple text file generated by Illumina tools - it has a specific format and is used by ZCall .
Build37ExtendedIlluminaManifest
A class to represent an 'Extended' Illumina Manifest file.
Build37ExtendedIlluminaManifestRecord
A class to represent a record (line) from an Extended Illumina Manifest [Assay] entry
Build37ExtendedIlluminaManifestRecord.Flag
Build37ExtendedIlluminaManifestRecordCreator
BuildBamIndex
Command line program to generate a BAM index (.bai) file from a BAM (.bam) file
ByIntervalListVariantContextIterator
Takes a VCFFileReader and an IntervalList and provides a single iterator over all variants in all the intervals.
CalculateFingerprintMetrics
Calculates various metrics on a sample fingerprint, indicating whether the fingerprint satisfies the assumptions we have.
CalculateReadGroupChecksum
CallingMetricAccumulator
Collects variants and generates metrics about them.
CallingMetricAccumulator.Result
CappedHaplotypeProbabilities
Casava18ReadNameEncoder
A read name encoder conforming to the standard described by Illumina Casava 1.8.
CbclData
This class provides that data structure for cbcls.
CbclReader
------------------------------------- CBCL Header ----------------------------------- Bytes 0 - 1 Version number, current version is 1 unsigned 16 bits little endian integer Bytes 2 - 5 Header size unsigned 32 bits little endian integer Byte 6 Number of bits per basecall unsigned Byte 7 Number of bits per q-score unsigned
CheckDuplicateMarking
CheckDuplicateMarking.Mode
CheckFingerprint
Checks the sample identity of the sequence/genotype data in the provided file (SAM/BAM or VCF) against a set of known genotypes in the supplied genotype file (in VCF format).
CheckIlluminaDirectory
Program to check a lane of an Illumina output directory.
CheckTerminatorBlock
Simple class to check the terminator block of a SAM file.
ChimeraUtil
CircularByteBuffer
Implementation of a circular byte buffer that uses a large byte[] internally and supports basic read/write operations from/to other byte[]s passed as arguments.
CleanSam
ClippingUtility
Utilities to clip the adapter sequence from a SAMRecord read
ClocsFileFaker
ClocsFileReader
The clocs file format is one of 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
ClusterCrosscheckMetrics
Summary
ClusterData
Store the information from Illumina files for a single cluster with one or more reads.
ClusterDataToSamConverter
Takes ClusterData provided by an IlluminaDataProvider into one or two SAMRecords, as appropriate, and optionally marking adapter sequence.
ClusteredCrosscheckMetric
A metric class to hold the result of `ClusterCrosscheckMetrics` fingerprints.
CollectAlignmentSummaryMetrics
A command line tool to read a BAM file and produce standard alignment metrics that would be applicable to any alignment.
CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
CollectArraysVariantCallingMetrics
Collects summary and per-sample metrics about variant calls in a VCF file.
CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
CollectBaseDistributionByCycle
CollectDuplicateMetrics
Collect DuplicateMark'ing metrics from an input file that was already Duplicate-Marked.
CollectGcBiasMetrics
Tool to collect information about GC bias in the reads in a given BAM file.
CollectHiSeqXPfFailMetrics
Collect metrics regarding the reason for reads (sequenced by HiSeqX) not passing the Illumina PF Filter.
CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
a metric class for describing FP failing reads from an Illumina HiSeqX lane *
CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
Metrics produced by the GetHiSeqXPFFailMetrics program.
CollectHiSeqXPfFailMetrics.ReadClassifier
CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
CollectHsMetrics
This tool takes a SAM/BAM file input and collects metrics that are specific for sequence datasets generated through hybrid-selection.
CollectIlluminaBasecallingMetrics
A Command line tool to collect Illumina Basecalling metrics for a sequencing run Requires a Lane and an input file of Barcodes to expect.
CollectIlluminaLaneMetrics
Command-line wrapper around `CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector`.
CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
Utility for collating Tile records from the Illumina TileMetrics file into lane-level and phasing-level metrics.
CollectIndependentReplicateMetrics
A CLP that, given a BAM and a VCF with genotypes of the same sample, estimates the rate of independent replication of reads within the bam.
CollectInsertSizeMetrics
Command line program to read non-duplicate insert sizes, create a Histogram and report distribution statistics.
CollectJumpingLibraryMetrics
Command-line program to compute metrics about outward-facing pairs, inward-facing pairs, and chimeras in a jumping library.
CollectMultipleMetrics
Class that is designed to instantiate and execute multiple metrics programs that extend SinglePassSamProgram while making only a single pass through the SAM file and supplying each program with the records as it goes.
CollectMultipleMetrics.Program
CollectMultipleMetrics.ProgramInterface
CollectOxoGMetrics
Class for trying to quantify the CpCG->CpCA error rate.
CollectOxoGMetrics.CpcgMetrics
Metrics class for outputs.
CollectQualityYieldMetrics
Command line program to calculate quality yield metrics
CollectQualityYieldMetrics.QualityYieldMetrics
A set of metrics used to describe the general quality of a BAM file
CollectQualityYieldMetrics.QualityYieldMetricsCollector
CollectQualityYieldMetrics.QualityYieldMetricsFlow
CollectRawWgsMetrics
Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments, same implementation as `CollectWgsMetrics`, with different defaults: lacks baseQ and mappingQ filters and has much higher coverage cap.
CollectRawWgsMetrics.RawWgsMetrics
CollectRnaSeqMetrics
CollectRrbsMetrics
Calculates and reports QC metrics for RRBS data based on the methylation status at individual C/G bases as well as CpG sites across all reads in the input BAM/SAM file.
CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
CollectSamErrorMetrics
Program to collect error metrics on bases stratified in various ways.
CollectSequencingArtifactMetrics
Quantify substitution errors caused by mismatched base pairings during various stages of sample / library prep.
CollectTargetedMetrics<METRIC extends MultilevelMetrics,COLLECTOR extends TargetMetricsCollector<METRIC>>
Both CollectTargetedPCRMetrics and CollectHsSelection share virtually identical program structures except for the name of their targeting mechanisms (e.g.
CollectTargetedPcrMetrics
This tool calculates a set of PCR-related metrics from an aligned SAM or BAM file containing targeted sequencing data.
CollectVariantCallingMetrics
Collects summary and per-sample metrics about variant calls in a VCF file.
CollectVariantCallingMetrics.VariantCallingDetailMetrics
A collection of metrics relating to snps and indels within a variant-calling file (VCF) for a given sample.
CollectVariantCallingMetrics.VariantCallingSummaryMetrics
A collection of metrics relating to snps and indels within a variant-calling file (VCF).
CollectWgsMetrics
Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
CollectWgsMetrics.WgsMetricsCollector
CollectWgsMetricsWithNonZeroCoverage
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
Metrics for evaluating the performance of whole genome sequencing experiments.
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
CombineGenotypingArrayVcfs
A simple program to combine multiple genotyping array VCFs into one VCF The input VCFs must have the same sequence dictionary and same list of variant loci.
CommandLineDefaults
Embodies defaults for global values that affect how the Picard Command Line operates.
CommandLineProgram
Abstract class to facilitate writing command-line programs.
CommandLineSyntaxTranslater
Class for handling translation of Picard-style command line argument syntax to POSIX-style argument syntax; used for running tests written with Picard style syntax against the Barclay command line parser.
CompareGtcFiles
A simple tool to compare two Illumina GTC files.
CompareMetrics
Compare two metrics files.
CompareMetrics.MetricComparisonDifferences
CompareSAMs
Rudimentary SAM comparer.
ConvertHaplotypeDatabaseToVcf
ConvertSequencingArtifactToOxoG
CounterManager
Class for managing a list of Counters of integer, provides methods to access data from Counters with respect to an offset.
CountingAdapterFilter
Counting filter that discards reads are unaligned or aligned with MQ==0 and whose 5' ends look like adapter Sequence
CountingDuplicateFilter
Counting filter that discards reads that have been marked as duplicates.
CountingFilter
A SamRecordFilter that counts the number of bases in the reads which it filters out.
CountingMapQFilter
Counting filter that discards reads below a configurable mapping quality threshold.
CountingPairedFilter
Counting filter that discards reads that are unpaired in sequencing and paired reads whose mates are not mapped.
CreateBafRegressMetricsFile
A simple program to create a standard picard metrics file from the output of bafRegress
CreateExtendedIlluminaManifest
Create an Extended Illumina Manifest by performing a liftover to Build 37.
CreateSequenceDictionary
Create a SAM/BAM file from a fasta containing reference sequence.
CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
CreateVerifyIDIntensityContaminationMetricsFile
A simple program to create a standard picard metrics file from the output of VerifyIDIntensity
CrosscheckFingerprints
Checks that all data in the set of input files appear to come from the same individual.
CrosscheckMetric
A class to hold the result of crosschecking fingerprints.
CrosscheckMetric.DataType
The data type.
CrosscheckMetric.FingerprintResult
CrosscheckReadGroupFingerprints
Deprecated.
6/6/2017 Use `CrosscheckFingerprints` instead.
CsvInputParser
DbSnpBitSetUtil
Utility class to use with DbSnp files to determine is a locus is a dbSnp site.
DbSnpBitSetUtil.DbSnpBitSets
Little tuple class to contain one bitset for SNPs and another for Indels.
DelimitedTextFileWithHeaderIterator
Iterate through a delimited text file in which columns are found by looking at a header line rather than by position.
DepthFilter
Filters out a record if all variant samples have depth lower than the given value.
DiagnosticsAndQCProgramGroup
Tools that collect sequencing quality-related and comparative metrics
DiploidGenotype
A genotype produced by one of the concrete implementations of AbstractAlleleCaller.
DiploidHaplotype
Simple enum to represent the three possible combinations of major/major, major/minor and minor/minor haplotypes for a diploid individual.
DiskBasedReadEndsForMarkDuplicatesMap
Disk-based implementation of ReadEndsForMarkDuplicatesMap.
DistanceMetric
DownsampleSam
Summary
DuplicationMetrics
Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords.
DuplicationMetricsFactory
Factory class that creates either regular or flow-based duplication metrics.
EarliestFragmentPrimaryAlignmentSelectionStrategy
When it is necessary to pick a primary alignment from a group of alignments for a read, pick the one that maps the earliest base in the read.
EmpiricalPhasingMetricsOutReader
EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
EmptyOutputArgumentCollection
ErrorMetric
Created by farjoun on 6/26/18.
ErrorSummaryMetrics
Summary metrics produced by `CollectSequencingArtifactMetrics` as a roll up of the context-specific error rates, to provide global error rates per type of base substitution.
EstimateLibraryComplexity
Attempts to estimate library complexity from sequence alone.
ExtractBarcodesProgram
ExtractFingerprint
Program to create a fingerprint for the contaminating sample when the level of contamination is both known and uniform in the genome.
ExtractIlluminaBarcodes
Determine the barcode for each read in an Illumina lane.
ExtractIlluminaBarcodes.PerTileBarcodeExtractor
Extracts barcodes and accumulates metrics for an entire tile.
ExtractSequences
Simple command line program that allows sub-sequences represented by an interval list to be extracted from a reference sequence file.
FastqToSam
Converts a FASTQ file to an unaligned BAM or SAM file.
FastWgsMetricsCollector
Class represents fast algorithm for collecting data from `AbstractLocusInfo` with a list of aligned `EdgingRecordAndOffset` objects.
FifoBuffer
Summary
FileFaker
FilterApplyingVariantIterator
Iterator that dynamically applies filter strings to VariantContext records supplied by an underlying iterator.
FilterFileFaker
Created by jcarey on 3/13/14.
FilterFileReader
Illumina uses an algorithm described in "Theory of RTA" that determines whether or not a cluster passes filter("PF") or not.
FilterSamReads
Summary
FilterSamReads.Filter
FilterVcf
Applies a set of hard filters to Variants and to Genotypes within a VCF.
FindMendelianViolations
Summary
Fingerprint
class to represent a genetic fingerprint as a set of HaplotypeProbabilities objects that give the relative probabilities of each of the possible haplotypes at a locus.
FingerprintChecker
Major class that coordinates the activities involved in comparing genetic fingerprint data whether the source is from a genotyping platform or derived from sequence data.
FingerprintIdDetails
class to hold the details of a element of fingerprinting PU tag
FingerprintingDetailMetrics
Detailed metrics about an individual SNP/Haplotype comparison within a fingerprint comparison.
FingerprintingSummaryMetrics
Summary fingerprinting metrics and statistics about the comparison of the sequence data from a single read group (lane or index within a lane) vs.
FingerprintMetrics
Class for holding metrics on a single fingerprint.
FingerprintResults
Class that is used to represent the results of comparing a read group within a SAM file, or a sample within a VCF against one or more set of fingerprint genotypes.
FingerprintUtils
A set of utilities used in the fingerprinting environment
FingerprintUtils.VariantContextSet
A class that holds VariantContexts sorted by genomic position
FisherStrandFilter
Filters records based on the phred scaled p-value from the Fisher Strand test stored in the FS attribute.
FixMateInformation
Summary
FixVcfHeader
Tool for replacing or fixing up a VCF header.
FlowBasedDuplicationMetrics
GA4GHScheme
The scheme is defined in the constructor.
GA4GHSchemeWithMissingAsHomRef
The default scheme is derived from the GA4GH Benchmarking Work Group's proposed evaluation scheme.
GatherBamFiles
Concatenate efficiently BAM files that resulted from a scattered parallel analysis.
GatherVcfs
Simple little class that combines multiple VCFs that have exactly the same set of samples and nonoverlapping sets of loci.
GATKBucketUtils
Copied from BucketUtils.java in GATK To be replaced once the original GATK BucketUtils.java is ported to htsjdk
GATKIOUtils
GATKUtils
GcBiasDetailMetrics
Class that holds detailed metrics about reads that fall within windows of a certain GC bin on the reference genome.
GcBiasMetrics
GcBiasMetricsCollector
Calculates GC Bias Metrics on multiple levels Created by kbergin on 3/23/15.
GcBiasSummaryMetrics
High level metrics that capture how biased the coverage in a certain lane is.
GcBiasUtils
Utilities to calculate GC Bias Created by kbergin on 9/23/15.
Gene
Holds annotation of a gene for storage in an OverlapDetector.
GeneAnnotationReader
Load gene annotations into an OverlapDetector of Gene objects.
GenotypeConcordance
Summary
GenotypeConcordance.Alleles
A simple structure to return the results of getAlleles.
GenotypeConcordanceContingencyMetrics
Class that holds metrics about the Genotype Concordance contingency tables.
GenotypeConcordanceCounts
A class to store the counts for various truth and call state classifications relative to a reference.
GenotypeConcordanceDetailMetrics
Class that holds detail metrics about Genotype Concordance
GenotypeConcordanceScheme
This defines for each valid TruthState and CallState tuple, the set of contingency table entries that to which the tuple should contribute.
GenotypeConcordanceSchemeFactory
Created by kbergin on 6/19/15.
GenotypeConcordanceStateCodes
Created by kbergin on 7/30/15.
GenotypeConcordanceStates
A class to store the various classifications for: 1.
GenotypeConcordanceStates.CallState
These states represent the relationship between the call genotype and the truth genotype relative to a reference sequence.
GenotypeConcordanceStates.ContingencyState
A specific state for a 2x2 contingency table.
GenotypeConcordanceStates.TruthAndCallStates
A minute class to store the truth and call state respectively.
GenotypeConcordanceStates.TruthState
These states represent the relationship between a truth genotype and the reference sequence.
GenotypeConcordanceSummaryMetrics
Class that holds summary metrics about Genotype Concordance
GenotypeFilter
An interface for classes that perform Genotype filtration.
GenotypeQualityFilter
Genotype filter that filters out genotypes below a given quality threshold.
GenotypingArraysProgramGroup
Miscellaneous tools, e.g.
GraphUtils
Created by farjoun on 11/2/16.
GraphUtils.Graph<Node extends Comparable<Node>>
GtcToVcf
Class to convert an Illumina GTC file into a VCF file.
GvcfMetricAccumulator
An accumulator for collecting metrics about a single-sample GVCF.
HaplotypeBlock
Represents information about a group of SNPs that form a haplotype in perfect LD with one another.
HaplotypeMap
A collection of metadata about Haplotype Blocks including multiple in memory "indices" of the data to make it easy to query the correct HaplotypeBlock or Snp by snp names, positions etc.
HaplotypeProbabilities
Abstract class for storing and calculating various likelihoods and probabilities for haplotype alleles given evidence.
HaplotypeProbabilities.Genotype
Log10(P(evidence| haplotype)) for the 3 different possible haplotypes {aa, ab, bb}
HaplotypeProbabilitiesFromContaminatorSequence
Represents the probability of the underlying haplotype of the contaminating sample given the data.
HaplotypeProbabilitiesFromGenotype
Represents a set of HaplotypeProbabilities that were derived from a single SNP genotype at a point in time.
HaplotypeProbabilitiesFromGenotypeLikelihoods
Represents the likelihood of the HaplotypeBlock given the GenotypeLikelihoods (GL field from a VCF, which is actually a log10-likelihood) for each of the SNPs in that block.
HaplotypeProbabilitiesFromSequence
Represents the probability of the underlying haplotype given the data.
HaplotypeProbabilityOfNormalGivenTumor
A wrapper class for any HaplotypeProbabilities instance that will assume that the given evidence is that of a tumor sample and provide an hp for the normal sample that tumor came from.
HelpConstants
HsMetricCollector
Calculates HS metrics for a given SAM or BAM file.
HsMetrics
Metrics generated by CollectHsMetrics for the analysis of target-capture sequencing experiments.
IdentifyContaminant
Program to create a fingerprint for the contaminating sample when the level of contamination is both known and uniform in the genome.
IlluminaAdpcFileWriter
A class to encompass writing an Illumina adpc.bin file.
IlluminaAdpcFileWriter.Record
IlluminaBasecallingMetrics
Metric for Illumina Basecalling that stores means and standard deviations on a per-barcode per-lane basis.
IlluminaBasecallsToFastq
IlluminaBasecallsToFastq.ReadNameFormat
Simple switch to control the read name format to emit.
IlluminaBasecallsToSam
IlluminaBasecallsToSam transforms a lane of Illumina data file formats (bcl, locs, clocs, qseqs, etc.) into SAM, BAM or CRAM file format.
IlluminaBPMFile
A class to parse the contents of an Illumina Bead Pool Manifest (BPM) file A BPM file contains metadata (including the alleles, mapping and normalization information) on an Illumina Genotyping Array Each type of genotyping array has a specific BPM .
IlluminaBPMLocusEntry
A simple class to represent a locus entry in an Illumina Bead Pool Manifest (BPM) file
IlluminaDataProviderFactory
IlluminaDataProviderFactory accepts options for parsing Illumina data files for a lane and creates an IlluminaDataProvider, an iterator over the ClusterData for that lane, which utilizes these options.
IlluminaDataType
List of data types of interest when parsing Illumina data.
IlluminaFileUtil
General utils for dealing with IlluminaFiles as well as utils for specific, support formats.
IlluminaFileUtil.SupportedIlluminaFormat
IlluminaGenotype
IlluminaLaneMetrics
Embodies characteristics that describe a lane.
IlluminaManifest
A class to represent an Illumina Manifest file.
IlluminaManifestRecord
A class to represent a record (line) from an Illumina Manifest [Assay] entry
IlluminaManifestRecord.IlluminaStrand
IlluminaMetricsCode
Illumina's TileMetricsOut.bin file codes various metrics, both concrete (all density id's are code 100) or as a base code (e.g.
IlluminaPhasingMetrics
Metrics for Illumina Basecalling that stores median phasing and prephasing percentages on a per-template-read, per-lane basis.
IlluminaReadNameEncoder
A read name encoder following the encoding initially produced by picard fastq writers.
IlluminaUtil
Misc utilities for working with Illumina specific files and data
IlluminaUtil.IlluminaAdapterPair
Describes adapters used on each pair of strands
IndelErrorCalculator
A calculator that estimates the error rate of the bases it observes for indels only.
IndelErrorMetric
Metric to be used for InDel errors
IndependentReplicateMetric
A class to store information relevant for biological rate estimation
InfiniumDataFile
A class to provide methods for accessing Illumina Infinium Data Files.
InfiniumEGTFile
A class to parse the contents of an Illumina Infinium cluster (EGT) file A cluster file contains information about the clustering information used in mapping red / green intensity information to genotype calls
InfiniumFileTOC
A class to encapsulate the table of contents for an Illumina Infinium Data Files.
InfiniumGTCFile
A class to parse the contents of an Illumina Infinium genotype (GTC) file A GTC file is the output of Illumina's genotype calling software (either Autocall or Autoconvert) and contains genotype calls, confidence scores, basecalls and raw intensities for all calls made on the chip.
InfiniumGTCRecord
InfiniumNormalizationManifest
A class to parse the contents of an Illumina Infinium Normalization Manifest file An Illumina Infinium Normalization Manifest file contains a subset of the information contained in the Illumina Manifest file in addition to the normalization ID which is needed for normalizating intensities in GtcToVcf
InfiniumTransformation
InfiniumVcfFields
A class to store fields that are specific to a VCF generated from an Illumina GTC file.
InfiniumVcfFields.GENOTYPE_VALUES
InsertSizeMetrics
Metrics about the insert size distribution of a paired-end library, created by the CollectInsertSizeMetrics program and usually written to a file with the extension ".insert_size_metrics".
InsertSizeMetricsCollector
Collects InsertSizeMetrics on the specified accumulationLevels using
IntensityChannel
The channels in a FourChannelIntensityData object, and the channels produced by a ClusterIntensityFileReader, for cases in which it is desirable to handle these abstractly rather than having the specific names in the source code.
IntervalArgumentCollection
Base interface for an interval argument collection.
IntervalListScatter
IntervalListScatterer
An interface for a class that scatters IntervalLists.
IntervalListScattererByBaseCount
a Baseclass for scatterers that scatter by uniqued base count.
IntervalListScattererByIntervalCount
Scatters `IntervalList` by interval count so that resulting `IntervalList`'s have the same number of intervals in them.
IntervalListScattererByIntervalCountWithDistributedRemainder
Scatters `IntervalList` by into `interval count` shards so that resulting `IntervalList`'s have approximately same number of intervals in them.
IntervalListScattererWithoutSubdivision
A BaseCount Scatterer that avoid breaking-up intervals.
IntervalListScattererWithoutSubdivisionWithOverflow
Like `IntervalListScattererWithoutSubdivision` but will overflow current list if the projected size of the remaining lists is bigger than the "ideal".
IntervalListScattererWithSubdivision
An IntervalListScatterer that attempts to place the same number of (uniquified) bases in each output interval list.
IntervalListScatterMode
An enum to control the creation of the various IntervalListScatter objects
IntervalListToBed
Trivially simple command line program to convert an IntervalList file to a BED file.
IntervalListTools
Performs various `IntervalList` manipulations.
IntervalListTools.Action
IntervalsManipulationProgramGroup
Tools that process genomic intervals in various formats.
Iterators
JumpingLibraryMetrics
High level metrics about the presence of outward- and inward-facing pairs within a SAM file generated with a jumping library, produced by the CollectJumpingLibraryMetrics program and usually stored in a file with the extension ".jump_metrics".
LanePhasingMetricsCollector
Helper class used to transform tile data for a lane into a collection of IlluminaPhasingMetrics
LibraryIdGenerator
A class to generate library Ids and keep duplication metrics by library IDs.
LiftOverHaplotypeMap
Liftover SNPs in HaplotypeMaps from one reference to another
LiftOverIntervalList
This tool adjusts the coordinates in an interval list on one reference to its homologous interval list on another reference, based on a chain file that describes the correspondence between the two references.
LiftoverUtils
LiftoverVcf
Summary
LocsFileFaker
Created by jcarey on 3/13/14.
LocsFileReader
The locs file format is one 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
LocusFunction
Describes the behavior of a locus relative to a gene.
MakeSitesOnlyVcf
Creates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.
MakeVcfSampleNameMap
Creates a TSV from sample name to VCF/GVCF path, with one line per input.
MarkDuplicates
A better duplication marking algorithm that handles all cases including clipped and gapped alignments.
MarkDuplicates.DuplicateTaggingPolicy
Enum used to control how duplicates are flagged in the DT optional tag on each read.
MarkDuplicates.DuplicateType
Enum for the possible values that a duplicate read can be tagged with in the DT attribute.
MarkDuplicatesForFlowArgumentCollection
MarkDuplicatesForFlowHelper
MarkDuplicates calculation helper class for flow based mode The class extends the behavior of MarkDuplicates which contains the complete code for the non-flow based mode.
MarkDuplicatesHelper
MarkDuplicatesWithMateCigar
An even better duplication marking algorithm that handles all cases including clipped and gapped alignments.
MarkDuplicatesWithMateCigarIterator
This will iterate through a coordinate sorted SAM file (iterator) and either mark or remove duplicates as appropriate.
MarkIlluminaAdapters
Command line program to mark the location of adapter sequences.
MarkQueue
This is the mark queue.
MatchResults
Represents the results of a fingerprint comparison between one dataset and a specific fingerprint file.
MathUtil
General math utilities
MathUtil.LogMath
A collection of common math operations that work with log values.
MeanQualityByCycle
Program to generate a data table and chart of mean quality by cycle from a BAM file.
MemoryBasedReadEndsForMarkDuplicatesMap
Map from String to ReadEnds object.
MendelianViolationMetrics
Describes the type and number of mendelian violations found within a Trio.
MendelianViolationsByFamily
Created by farjoun on 6/25/16.
MergeableMetricBase
An extension of MetricBase that knows how to merge-by-adding fields that are appropriately annotated (`MergeByAdding`).
MergeableMetricBase.MergeByAdding
Metrics whose values can be merged by adding.
MergeableMetricBase.MergeByAssertEquals
Metrics whose values should be equal when merging.
MergeableMetricBase.MergingIsManual
Metrics that are merged manually in the `MergeableMetricBase.merge(MergeableMetricBase)` ()}.
MergeableMetricBase.NoMergingIsDerived
Metrics that are not merged, but are subsequently derived from other metrics, for example by `MergeableMetricBase.calculateDerivedFields()`.
MergeableMetricBase.NoMergingKeepsValue
Metrics that are not merged.
MergeBamAlignment
Summary
MergePedIntoVcf
Class to take genotype calls from a ped file output from zCall and merge them into a vcf from autocall.
MergeSamFiles
This tool is used for combining SAM and/or BAM files from different runs or read groups into a single file, similar to the \"merge\" function of Samtools (http://www.htslib.org/doc/samtools.html).
MergeVcfs
Combines multiple variant files into a single variant file.
MetricAccumulationLevel
For use with Picard metrics programs that may output metrics for multiple levels of aggregation with an analysis.
MMapBackedIteratorFactory
MMapBackedIteratorFactory a file reader that takes a header size and a binary file, maps the file to a read-only byte buffer and provides methods to retrieve the header as it's own bytebuffer and create iterators of different data types over the values of file (starting after the end of the header).
MostDistantPrimaryAlignmentSelectionStrategy
For a paired-end aligner that aligns each end independently, select the pair of alignments that result in the largest insert size.
MultiLevelCollector<METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,Histogram_KEY extends Comparable,ARGTYPE>
MultiLevelCollector handles accumulating Metrics at different MetricAccumulationLevels(ALL_READS, SAMPLE, LIBRARY, READ_GROUP).
MultilevelMetrics
MultiTileBclFileFaker
Created by jcarey on 3/13/14.
MultiTileBclFileUtil
NextSeq-style bcl's have all tiles for a cycle in a single file.
MultiTileBclParser
Parse .bcl.bgzf files that contain multiple tiles in a single file.
MultiTileFileUtil<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData>
For file types for which there is one file per lane, with fixed record size, and all the tiles in it, so the s_<lane>.bci file can be used to figure out where each tile starts and ends.
MultiTileFilterParser
Read filter file that contains multiple tiles in a single file.
MultiTileLocsFileFaker
Created by jcarey on 3/13/14.
MultiTileLocsParser
Read locs file that contains multiple tiles in a single file.
MultiTileParser<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData>
Abstract class for files with fixed-length records for multiple tiles, e.g.
NonNFastaSize
A tool to count the number of non-N bases in a fasta file
NormalizeFasta
Little program to "normalize" a fasta file to ensure that all line of sequence are the same length, and are a reasonable length!
OpticalDuplicateFinder
Contains methods for finding optical/co-localized/sequencing duplicates.
OptionalReferenceArgumentCollection
Picard default argument collection for an optional reference.
OtherProgramGroup
Miscellaneous tools, e.g.
OutputArgumentCollection
Base interface for an output argument collection.
OutputMapping
In multiple locations we need to know what cycles are output, as of now we output all non-skip cycles, but rather than sprinkle this knowledge throughout the parser code, instead OutputMapping provides all the data a client might want about the cycles to be output including what ReadType they are.
OverlappingErrorMetric
An error metric for the errors invovling bases in the overlapping region of a read-pair.
OverlappingReadsErrorCalculator
A calculator that estimates the error rate of the bases it observes, assuming that the reference is truth.
Pair<X extends Comparable<X>,Y extends Comparable<Y>>
Simple Pair class.
PairedVariantSubContextIterator
An iterator that takes a pair of iterators over VariantContexts and iterates over them in tandem.
PairedVariantSubContextIterator.VcfTuple
Little class to hold a pair of VariantContexts that are in sync with one another.
PanelMetricsBase
A base class for Metrics for targeted panels.
ParameterizedFileUtil
PathProvider
A class whose purpose is to initialize the various plugins that provide Path support.
PedFile
Represents a .ped file of family information as documented here: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml Stores the information in memory as a map of individualId -> Pedigree information for that individual
PerTileFileUtil
PerTileOrPerRunFileUtil
PerTileParser<ILLUMINA_DATA extends picard.illumina.parser.IlluminaData>
Abstract base class for Parsers that open a single tile file at a time and iterate through them.
PerTilePerCycleFileUtil
PerUnitMetricCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,HKEY extends Comparable,ARGTYPE>
PerRecordCollector - An interface for classes that collect data in order to generate one or more metrics.
PGTagArgumentCollection
Argument Collection which holds parameters common to classes that want to add PG tags to reads in SAM/BAM files
PhysicalLocation
Small interface that provides access to the physical location information about a cluster.
PhysicalLocationForMateCigar
Stores the minimal information needed for optical duplicate detection.
PhysicalLocationForMateCigarSet
This stores records that are comparable for detecting optical duplicates.
PhysicalLocationInt
Small class that provides access to the physical location information about a cluster.
PhysicalLocationShort
Small class that provides access to the physical location information about a cluster.
PicardCommandLine
This is the main class of Picard and is the way of executing individual command line programs.
PicardException
Basic Picard runtime exception that, for now, does nothing much
PicardHtsPath
A Subclass of `HtsPath` with conversion to `Path` making use of `IOUtil`
PosFileFaker
Created by jcarey on 3/13/14.
PosFileReader
The pos file format is one 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
PositionBasedDownsampleSam
Summary
PosParser
PosParser parses multiple files formatted as one of the three file formats that contain position information only (pos, locs, and clocs).
PredicateFilterDecoratingClosableIterator<T>
Performs on-the-fly filtering of the provided `VariantContext` `Iterator` such that only variants that satisfy all predicates are emitted.
PrimaryAlignmentKey
It is useful to define a key such that the key will occur at most once among the primary alignments in a given file (assuming the file is valid).
PrimaryAlignmentSelectionStrategy
Given a set of alignments for a read or read pair, mark one alignment as primary, according to whatever strategy is appropriate.
PropertyUtils
Utility for loading properties files from resources.
QdFilter
Filters out sites that have a QD annotation applied to them and where the QD value is lower than a lower limit.
QualityScoreDistribution
Charts quality score distribution within a BAM file.
QuerySortedReadPairIteratorUtil
A collection of helper utilities for iterating through reads that are in query-name sorted read order as pairs
QuerySortedReadPairIteratorUtil.ReadPair
Range
While structurally identical to CompositeIndex, this class is maintained as it makes code more readable when the two are used together (see QSeqParser)
ReadBaseStratification
Classes, methods, and enums that deal with the stratification of read bases and reference information.
ReadBaseStratification.BinnedReadCycleStratifier
Stratifies into quintiles of read cycle.
ReadBaseStratification.CigarOperatorsInReadStratifier
Stratifies according to the number of matching cigar operators (from CIGAR string) that the read has.
ReadBaseStratification.CollectionStratifier
A CollectionStratifier is a stratifier that uses a collection of stratifiers to inform the stratification.
ReadBaseStratification.Consensus
Types of consensus reads as determined by the number of duplicates used from first and second strands.
ReadBaseStratification.ConsensusStratifier
Stratify by tags used during duplex and single index consensus calling.
ReadBaseStratification.CycleBin
An enum designed to hold a binned version of any probability-like number (between 0 and 1) in quintiles
ReadBaseStratification.FlowCellTileStratifier
Stratifies base into their read's tile which is parsed from the read-name.
ReadBaseStratification.FlowCellXStratifier
Stratifies base into their read's X coordinate which is parsed from the read-name.
ReadBaseStratification.FlowCellYStratifier
Stratifies base into their read's Y coordinate which is parsed from the read-name.
ReadBaseStratification.GCContentStratifier
A stratifier that uses GC (of the read) to stratify.
ReadBaseStratification.IndelLengthStratifier
Stratifies according to the length of an insertion or deletion.
ReadBaseStratification.IndelsInReadStratifier
Stratifies according to the number of indel bases (from CIGAR string) that the read has.
ReadBaseStratification.LongShortHomopolymer
ReadBaseStratification.LongShortHomopolymerStratifier
Stratify bases according to the type of Homopolymer that they belong to (repeating element, final reference base and whether the length is "long" or not).
ReadBaseStratification.MismatchesInReadStratifier
Stratifies according to the overall mismatches (from `SAMTag.NM`) that the read has against the reference, NOT including the current base.
ReadBaseStratification.NsInReadStratifier
Stratify by the number of Ns found in the read.
ReadBaseStratification.PairOrientation
An enum for holding a reads read-pair's Orientation (i.e.
ReadBaseStratification.PairStratifier<T extends Comparable<T>,R extends Comparable<R>>
A PairStratifier is a stratifier that uses two other stratifiers to inform the stratification.
ReadBaseStratification.ProperPaired
An enum to hold information about the "properness" of a read pair
ReadBaseStratification.ReadDirection
An enum for holding the direction for a read (positive strand or negative strand
ReadBaseStratification.ReadOrdinality
An enum to hold the ordinality of a read
ReadBaseStratification.RecordAndOffsetStratifier<T extends Comparable<T>>
The main interface for a stratifier.
ReadData
Data for a single end of a paired-end read, a barcode read, or for the entire read if not paired end.
ReadDataManipulationProgramGroup
Tools that manipulate read data in SAM, BAM or CRAM format
ReadDescriptor
Represents one set of cycles in an ReadStructure (e.g.
ReadEnds
Little struct-like class to hold read pair (and fragment) end data for duplicate marking.
ReadEndsForMarkDuplicates
Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar
ReadEndsForMarkDuplicatesCodec
Codec for ReadEnds that just outputs the primitive fields and reads them back.
ReadEndsForMarkDuplicatesMap
Interface for storing and retrieving ReadEnds objects.
ReadEndsForMarkDuplicatesWithBarcodes
ReadEndsForMarkDuplicatesWithBarcodesCodec
Created by nhomer on 9/13/15.
ReadEndsForMateCigar
A class to store individual records for MarkDuplicatesWithMateCigar.
ReadNameEncoder
ReadNameParser
Provides access to the physical location information about a cluster.
ReadStructure
Describes the intended logical output structure of clusters of an Illumina run.
ReadType
A read type describes a stretch of cycles in an ReadStructure (e.g.
ReferenceArgumentCollection
Base interface for a reference argument collection.
ReferenceProgramGroup
Tools that analyze and manipulate FASTA format references
RefFlatReader
Loads gene annotations from a refFlat file into an OverlapDetector<Gene>.
RefFlatReader.RefFlatColumns
ReflectionUtil
Class which contains utility functions that use reflection.
RenameSampleInVcf
Renames a sample within a VCF or BCF.
ReorderSam
Reorders a SAM/BAM input file according to the order of contigs in a second reference file.
ReplaceSamHeader
RepresentativeReadIndexer
Little struct-like class to hold a record index, the index of the corresponding representative read, and duplicate set size information.
RepresentativeReadIndexerCodec
Codec for read names and integers that outputs the primitive fields and reads them back.
RequiredOutputArgumentCollection
RequiredReferenceArgumentCollection
Argument collection for references that are required (and not common).
RevertOriginalBaseQualitiesAndAddMateCigar
This tool reverts the original base qualities (if specified) and adds the mate cigar tag to mapped SAM, BAM or CRAM files.
RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
Used as a return for the canSkipSAMFile function.
RevertSam
Reverts a SAM file by optionally restoring original quality scores and by removing all alignment information.
RevertSam.FileType
RExecutor
Util class for executing R scripts.
RnaSeqMetrics
Metrics about the alignment of RNA-seq reads within a SAM file to genes, produced by the CollectRnaSeqMetrics program and usually stored in a file with the extension ".rna_metrics".
RnaSeqMetricsCollector
RnaSeqMetricsCollector.StrandSpecificity
RrbsCpgDetailMetrics
Holds information about CpG sites encountered for RRBS processing QC
RrbsMetricsCollector
RrbsSummaryMetrics
Holds summary statistics from RRBS processing QC
SamAlignmentMerger
Class that takes in a set of alignment information in SAM format and merges it with the set of all reads for which alignment was attempted, stored in an unmapped SAM file.
SamComparison
Compare two SAM/BAM files.
SamComparison.AlignmentComparison
SAMComparisonArgumentCollection
Argument collection for SAM comparison
SamComparisonMetric
Metric for results of SamComparison.
SamFormatConverter
Converts a BAM file to human-readable SAM output or vice versa
SAMRecordAndReference
SAMRecordAndReferenceMultiLevelCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,HKEY extends Comparable>
SAMRecordMultiLevelCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,HKEY extends Comparable>
Defines a MultilevelPerRecordCollector using the argument type of SAMRecord so that this doesn't have to be redefined for each subclass of MultilevelPerRecordCollector
SamRecordWithOrdinalAndSetDuplicateReadFlag
This class sets the duplicate read flag as the result state when examining sets of records.
SamToBfqWriter
Class to take unmapped reads in SAM/BAM/CRAM file format and create Maq binary fastq format file(s) -- one or two of them, depending on whether it's a paired-end read.
SamToFastq
Extracts read sequences and qualities from the input SAM/BAM file and writes them into the output file in Sanger FASTQ format.
SamToFastqWithTags
Extracts read sequences and qualities from the input SAM/BAM file and SAM/BAM tags and writes them into output files in Sanger FASTQ format.
ScatterIntervalsByNs
A Tool for breaking up a reference into intervals of alternating regions of N and ACGT bases.
ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
SequenceDictionaryUtils
Class with helper methods for generating and writing SequenceDictionary objects.
SequenceDictionaryUtils.SamSequenceRecordsIterator
SequencingArtifactMetrics
SequencingArtifactMetrics.BaitBiasDetailMetrics
Bait bias artifacts broken down by context.
SequencingArtifactMetrics.BaitBiasSummaryMetrics
Summary analysis of a single bait bias artifact, also known as a reference bias artifact.
SequencingArtifactMetrics.PreAdapterDetailMetrics
Pre-adapter artifacts broken down by context.
SequencingArtifactMetrics.PreAdapterSummaryMetrics
Summary analysis of a single pre-adapter artifact.
SetNmAndUqTags
Deprecated.
SetNmMdAndUqTags
Fixes the NM, MD, and UQ tags in a SAM or BAM file.
Sex
Represents the sex of an individual.
SimpleErrorCalculator
A calculator that estimates the error rate of the bases it observes, assuming that the reference is truth.
SimpleMarkDuplicatesWithMateCigar
This is a simple tool to mark duplicates using the DuplicateSetIterator, DuplicateSet, and SAMRecordDuplicateComparator.
SingleBarcodeDistanceMetric
A class for finding the distance between a single barcode and a barcode-read (with base qualities)
SinglePassSamProgram
Super class that is designed to provide some consistent structure between subclasses that simply iterate once over a coordinate sorted BAM and collect information from the records as the go in order to produce some kind of output.
Snp
Class to represent a SNP in context of a haplotype block that is used in fingerprinting.
SortedBasecallsConverter<CLUSTER_OUTPUT_RECORD>
SortedBasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).
SortGff
Summary
SortSam
Sorts a SAM or BAM file.
SortVcf
Sorts one or more VCF files according to the order of the contigs in the header/sequence dictionary and then by coordinate.
SplitSamByLibrary
Command-line program to split a SAM/BAM/CRAM file into separate files based on library name.
SplitSamByNumberOfReads
Splits the input queryname sorted or query-grouped SAM/BAM/CRAM file and writes it into multiple BAM files, each with an approximately equal number of reads.
SplitVcfs
Splits the input VCF file into two, one for indels and one for SNPs.
StandardOptionDefinitions
A set of String constants in which the name of the constant (minus the _SHORT_NAME suffix) is the standard long Option name, and the value of the constant is the standard shortName.
TabbedInputParser
Parser for tab-delimited files
TabbedTextFileWithHeaderParser
Parse a tabbed text file in which columns are found by looking at a header line rather than by position.
TargetedPcrMetrics
Metrics class for the analysis of reads obtained from targeted pcr experiments e.g.
TargetedPcrMetricsCollector
Calculates HS metrics for a given SAM or BAM file.
TargetMetrics
TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA).
TargetMetricsBase
TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA).
TargetMetricsCollector<METRIC_TYPE extends MultilevelMetrics>
TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA).
TargetMetricsCollector.Coverage
A simple class that is used to store the coverage information about an interval.
Test
Testing
For internal test purposes only.
TheoreticalSensitivity
Created by David Benjamin on 5/13/15.
TheoreticalSensitivity.RouletteWheel
TheoreticalSensitivityMetrics
TheoreticalSensitivityMetrics, are metrics calculated from TheoreticalSensitivity and parameters used in the calculation.
ThreadPoolExecutorUtil
ThreadPoolExecutorWithExceptions
This version of the thread pool executor will throw an exception if any of the internal jobs have throw exceptions while executing
Tile
Represents a tile from TileMetricsOut.bin.
TileIndex
Load a file containing 8-byte records like this: tile number: 4-byte int number of clusters in tile: 4-byte int Number of records to read is determined by reaching EOF.
TileIndex.TileIndexRecord
TileMetricsOutReader
Reads a TileMetricsOut file commonly found in the InterOp directory of an Illumina Run Folder.
TileMetricsOutReader.IlluminaLaneTileCode
Helper class which captures the combination of a lane, tile & metric code
TileMetricsOutReader.IlluminaTileMetrics
IlluminaPhasingMetrics corresponds to a single record in a TileMetricsOut file
TileMetricsOutReader.TileMetricsVersion
TileMetricsUtil
Utility for reading the tile data from an Illumina run directory's TileMetricsOut.bin file
TilePhasingValue
Captures information about a phasing value - Which read it corresponds to, which phasing type and a median value
TileTemplateRead
Defines the first or second template read for a tile
Transition
Enum representation of a transition from one base to any other.
Transition.Base
UmiAwareMarkDuplicatesWithMateCigar
This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.
UmiGraph
UmiGraph is used to identify UMIs that come from the same original source molecule.
UmiMetrics
Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords using the UmiAwareDuplicateSetIterator.
UnsignedTypeUtil
A utility class for dealing with unsigned types.
UnsortedBasecallsConverter<CLUSTER_OUTPUT_RECORD>
UnortedBasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).
UpdateVcfSequenceDictionary
Takes a VCF file and a Sequence Dictionary (from a variety of file types) and updates the Sequence Dictionary in VCF.
ValidateSamFile
This tool reports on the validity of a SAM or BAM file relative to the SAM format specification.
ValidateSamFile.Mode
VariantAccumulatorExecutor<ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>,RESULT>
Describes the functionality for an executor that manages the delegation of work to `VariantProcessor.Accumulator`s.
VariantAccumulatorExecutor.MultiThreadedChunkBased<A extends VariantProcessor.Accumulator<R>,R>
A `VariantAccumulatorExecutor` that breaks down work into chunks described by the provided `VariantIteratorProducer` and spreads them over the indicated number of threads.
VariantEvaluationProgramGroup
Tools that evaluate and refine variant calls, e.g.
VariantFilter
Interface for classes that can generate filters for VariantContexts.
VariantFilteringProgramGroup
Tools that filter variants
VariantIteratorProducer
A mechanism for iterating over `CloseableIterator` of `VariantContext`s in in some fashion, given VCF files and optionally an interval list.
VariantManipulationProgramGroup
Tools that manipulate variant call format (VCF) data
VariantProcessor<RESULT,ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>>
Describes an object that processes variants and produces a result.
VariantProcessor.Accumulator<RESULT>
Handles `VariantContext`s, and accumulates their data in some fashion internally.
VariantProcessor.AccumulatorGenerator<ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>,RESULT>
Generates instances of `VariantProcessor.Accumulator`s.
VariantProcessor.Builder<A extends VariantProcessor.Accumulator<R>,R>
Simple builder of `VariantProcessor`s.
VariantProcessor.ResultMerger<RESULT>
Takes a collection of results produced by `VariantProcessor.Accumulator.result()` and merges them into a single RESULT.
VariantType
Enum to hold the possible types of dbSnps.
VcfFileSegment
Deprecated.
from 2022-03-17, Use VcfPathSegment
VcfFileSegmentGenerator
Deprecated.
from 2022-03-17, Use `VcfPathSegmentGenerator`
VcfFormatConverter
Converts an ASCII VCF file to a binary BCF or vice versa.
VcfPathSegment
Describes a segment of a particular VCF file.
VcfPathSegmentGenerator
Describes a mechanism for producing `VcfPathSegment`s from a VCF file path.
VcfToAdpc
A simple program to convert a Genotyping Arrays VCF to an ADPC file (Illumina intensity data file).
VcfToIntervalList
Converts a VCF or BCF file to a Picard Interval List.
VcfToIntervalList.VARIANT_ID_TYPES
VcfUtils
Created by farjoun on 4/1/17.
VerifyIDIntensityContaminationMetrics
ViewSam
Prints a SAM or BAM file to the screen.
ViewSam.AlignmentStatus
ViewSam.PfStatus
WgsMetrics
Metrics for evaluating the performance of whole genome sequencing experiments.
WgsMetricsProcessor
Interface for processing data and generate result for CollectWgsMetrics
WgsMetricsProcessorImpl<T extends htsjdk.samtools.util.AbstractRecordAndOffset>
Implementation of `WgsMetricsProcessor` that gets input data from a given iterator and processes it with a help of collector